Dinoflagellates are microscopic single-celled planktonic organisms that used to be classified as algae but are now considered to be in a large and diverse group known as Chromalveolata. They can be free-living or can be present in large number in the tissues of a host. The motile, mastigote stage in the water column has two flagella and a characteristic method of swimming, while inside a host it metamorphoses into a spherical, non-motile, coccoid stage without any flagella. Zooxanthellae are photosynthetic organisms, which contain chlorophyll a and chlorophyll c, as well as the dinoflagellate pigments peridinin and diadinoxanthin. These provide the yellowish and brownish colours typical of many of the host species.[2] During the day, they provide their host with the organic carbon products of photosynthesis, sometimes providing up to 90% of their host's energy needs for metabolism, growth and reproduction. In return, they receive nutrients, carbon dioxide, and an elevated position with access to sunshine.[3][4]

A juvenile organism or newly established colony can acquire its zooxanthellae via sexual reproduction or directly from the environment. The egg from which the individual developed may have already been infected by zooxanthellae at the time of fertilisation, or cells of the symbiont may have been transferred from the mother in a period during which the larva was brooded by its parent. Alternatively, the new individual may acquire the zooxanthellae direct from sea water in which the dinoflagellates freely live at some stages of their life cycle. Some stony corals use chemotaxis, with infection occurring as a result of the emission by the coral of a chemical attractant. Infection may also occur after ingestion of infected faecal matter by the host, or of prey that already houses the symbionts. Such indirect acquisition can result in the new host being infected by a species of zooxanthella different from that present in its parent,[2] and a bleached coral that has expelled its zooxanthellae may be recolonised by another species perhaps more suited to the stressors present in the environment.[4]